Integrated analysis of coding genes and non-coding RNAs during hair follicle cycle of cashmere goat (Capra hircus)

• Published in: BMC genomics Vol. 18; no. 1; pp. 767 - 13
• Main Authors: Wang, Shanhe, Ge, Wei, Luo, Zhixin, Guo, Yang, Jiao, Beilei, Qu, Lei, Zhang, Zhiying, Wang, Xin
• Format: Journal Article
• Language: English
• Published: London BioMed Central 11.10.2017; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Anagen; Animal Genetics and Genomics; Animals; Annotations; Bioinformatics; Biology; Biomedical and Life Sciences; Capra hircus; Cashmere; Cashmere goat; Cycles; Enzymes; GATA-3 protein; Gene expression; Genes; Genetic aspects; Genomes; Genomics; Goats; Growth factors; Hair; Hair follicle; Hair follicles; Homeostasis; Life Sciences; lncRNA; Microarrays; Microbial Genetics and Genomics; MicroRNAs; miRNA; mRNA; Next-generation sequencing; Non-coding RNA; Non-human and non-rodent vertebrate genomics; Physiological aspects; Plant Genetics and Genomics; Proteins; Proteomics; Quality; Research Article; Ribonucleic acid; RNA; Skin; Smad3 protein; Software; Telogen; United States > US; China; Hair follicle; miRNA; Anagen; lncRNA; Cashmere goat; Telogen
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-017-4145-0

Background Cashmere growth is a seasonal and cyclic phenomenon under the control of photoperiod and multiple stimulatory and inhibitory signals. Beyond relevant coding genes, microRNA (miRNA) and long non coding RNA (lncRNA) play an indispensable role in hair follicle (HF) development and skin homeostasis. Furthermore, the influence of lncRNA upon miRNA function is also rapidly emerging. However, little is known about miRNAs, lncRNAs and their functions as well as their interactions on cashmere development and cycling. Result Here, based on lncRNA and miRNA high-throughput sequencing and bioinformatics analysis, we have identified 1108 lncRNAs and 541 miRNAs in cashmere goat skin during anagen and telogen. Compared with telogen, 1388 coding genes, 41 lncRNAs and 15 miRNAs were upregulated, while 1104 coding genes, 157 lncRNAs and 8 miRNAs were downregulated in anagen (adjusted P -value ≤0.05 and relative fold-change ≥2). Subsequently, we investigated the impact of lncRNAs on their target genes in cis and trans, indicating that these lncRNAs are functionally conserved during HF development and cycling. Furthermore, miRNA-mRNA and miRNA-lncRNA interaction were identified through the bioinformatics algorithm miRanda, then the ceRNA networks, miR-221-5p-lnc_000679- WNT3 , miR-34a-lnc_000181- GATA3 and miR-214-3p-lnc_000344- SMAD3 , were constructed under defined rules, to illustrate their roles in cashmere goat HF biology. Conclusion The present study provides a resource for lncRNA, miRNA and mRNA studies in cashmere cycling and development. We also demonstrate potential ceRNA regulatory networks in cashmere goat HF cycling for the first time. It expands our knowledge about lncRNA and miRNA biology as well as contributes to the annotation of the goat genome.